public override bool PrepareOptions()
{
if (!string.IsNullOrWhiteSpace(ContaminantFile) && !File.Exists(ContaminantFile))
{
ParsingErrors.Add(string.Format("Contaminant file not exists: {0}", ContaminantFile));
}
if (!File.Exists(InputFile))
{
ParsingErrors.Add(string.Format("Input file not exists: {0}", InputFile));
}
if (string.IsNullOrWhiteSpace(this.OutputFile))
{
if (ReversedOnly)
{
OutputFile = FileUtils.ChangeExtension(InputFile, this.DecoyKey + "_ONLY.fasta");
}
else
{
OutputFile = FileUtils.ChangeExtension(InputFile, this.DecoyKey + ".fasta");
}
}
if (IsPseudoAminoacid)
{
PseudoAminoacidBuilder = new PseudoSequenceBuilder(PseudoAminoacids, IsPseudoForward);
}
return(ParsingErrors.Count == 0);
}
public ReversedDatabaseBuilderOptions()
{
ReversedOnly = false;
IsPseudoAminoacid = true;
PseudoAminoacids = "KR";
IsPseudoForward = false;
ContaminantFile = string.Empty;
PseudoAminoacidBuilder = null;
this.DecoyKey = "REVERSED";
this.DecoyType = DecoyType.Start;
}